How simple can a model of an empty viral capsid be? Charge distributions in viral capsids

We investigate and quantify salient features of the charge distributions on viral capsids. Our analysis combines the experimentally determined capsid geometry with simple models for ionization of amino acids, thus yielding the detailed description of spatial distribution for positive and negative charge across the capsid wall. The obtained data is processed in order to extract the mean radii of distributions, surface charge densities and dipole moment densities. The results are evaluated and examined in light of previously proposed models of capsid charge distributions, which are shown to have to some extent limited value when applied to real viruses.Comment: 10 pages, 10 figures; accepted for publication in Journal of Biological Physic

1971

Shop Talk by Frank Santos (page 1) You\u27ve Come a Long Way, Lawn-Mower Pusher by Alan B. Albin (2) In The Eyes of the Laymen by Eugene P. Elcik (2) The Importance of Water Management by Fred V. Grau (A-1) Automatic Irrigation Systems Integrated with Pumping Systems by Michael O. Mattwell (A-5) Installation of a Complete Water Source and Automatic System by Richard C. Blake (A-19) How the Soil Conservation Service Can Help in Golf Course Management by Christopher G. Mousitakis (A-22) Our Shrinking Environment by Haim B. Gunner (A-24) Pesticides\u27 Dilemma - Emotion vs. Science by Allen H. Morgan (A-28) Effects of Turf Grasses and Trees in Neutralizing Waste Water by William E. Sopper (A-34) Unsolved and New Problems Developing in Golf Course Management by Alexander M. Radko (A-44) Coming of the Conglomerate Director of Golf Courses by Edmund B. Ault (A-48) Aquatic Weed Control by John E. Gallagher (A-52) What Project Apollo Has Done for Golf and Golf Course Architecture by Mal Purdy (A-54) Maintenance of Grass Tennis Courts by Wayne Zoppo (A-59) Diseases of Ornametnals Growing in Turf Areas by R.E. Partyka (A-62) Control of Turf Insects by John C. Schread (A-65) Lime for Turf by Henry W. Indyk (A-68) How to Stop Guessing When You Buy Seed by Dale Kern (A-71) Broad Aspects of Turf Grass Culture Other Than Golf Courses by Geoffrey S. Cornish (A-79) Establishing and Maintaining Turf int he national Capitol Parks by Alton E. Rabbitt (A-81) Preventive Maintenance on Small One Cylinder Air Cooled Engine by F. W. Hazle (A-85) Top Fairway Mower Performance by James R. Maloney (A-95) Grinding Reel Type Mowers by Ray Christopherson (A-99

Slow Dissociation of a Charged Ligand: Analysis of the Primary Quinone QA Site of Photosynthetic Bacterial Reaction Centers

Reaction centers (RCs) are integral membrane proteins that undergo a series of electron transfer reactions during the process of photosynthesis. In the QA site of RCs from Rhodobacter sphaeroides, ubiquinone-10 is reduced, by a single electron transfer, to its semiquinone. The neutral quinone and anionic semiquinone have similar affinities, which is required for correct in situ reaction thermodynamics. A previous study showed that despite similar affinities, anionic quinones associate and dissociate from the QA site at rates ≈104 times slower than neutral quinones indicating that anionic quinones encounter larger binding barriers (Madeo, J.; Gunner, M. R. Modeling binding kinetics at the QA site in bacterial reaction centers. Biochemistry2005, 44, 10994–11004). The present study investigates these barriers computationally, using steered molecular dynamics (SMD) to model the unbinding of neutral ground state ubiquinone (UQ) and its reduced anionic semiquinone (SQ–) from the QA site. In agreement with experiment, the SMD unbinding barrier for SQ– is larger than for UQ. Multi Conformational Continuum Electrostatics (MCCE), used here to calculate the binding energy, shows that SQ– and UQ have comparable affinities. In the QA site, there are stronger binding interactions for SQ– compared to UQ, especially electrostatic attraction to a bound non-heme Fe2+. These interactions compensate for the higher SQ– desolvation penalty, allowing both redox states to have similar affinities. These additional interactions also increase the dissociation barrier for SQ– relative to UQ. Thus, the slower SQ– dissociation rate is a direct physical consequence of the additional binding interactions required to achieve a QA site affinity similar to that of UQ. By a similar mechanism, the slower association rate is caused by stronger interactions between SQ– and the polar solvent. Thus, stronger interactions for both the unbound and bound states of charged and highly polar ligands can slow their binding kinetics without a conformational gate. Implications of this for other systems are discussed

High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a highresolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation